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The systems biology simulation core algorithm

Roland Keller, Alexander Dörr, Akito Tabira, Akira Funahashi, Michael J Ziller, Richard Adams, Nicolas Rodriguez, Nicolas Novère, Noriko Hiroi, Hannes Planatscher, Andreas Zell, Andreas Dräger
2013 BMC Systems Biology  
systems biology.  ...  We provide a flexible reference implementation as part of the Systems Biology Simulation Core Library, a community-driven project providing a large collection of numerical solvers and a sophisticated interface  ...  Acknowledgements The authors are grateful to B. Kotcon  ... 
doi:10.1186/1752-0509-7-55 pmid:23826941 pmcid:PMC3707837 fatcat:zhjofmi5yzfancc432ca2vljwi

StochSoCs: High Performance Biocomputing Simulations for Large Scale Systems Biology

Elias S. Manolakos, Elias Kouskoumvekakis
2017 2017 International Conference on High Performance Computing & Simulation (HPCS)  
The stochastic simulation of large-scale biochemical reaction networks is of great importance for systems biology since it enables the study of inherently stochastic biological mechanisms at the whole  ...  The workers are implemented using multi-core and many-core processors, or FPGA accelerators that can handle the simulation of thousands of stochastic repetitions of complex biomodels, with possibly thousands  ...  Manolakos) co-funded by the EU (European Social Fund) and GSRT national resources.  ... 
doi:10.1109/hpcs.2017.156 dblp:conf/ieeehpcs/ManolakosK17 fatcat:h6qikcwgvna2jdyxtzn37z3vom

The Systems Biology Simulation Core Library

Hemil Panchiwala, Shalin Shah, Hannes Planatscher, Mykola Zakharchuk, Matthias König, Andreas Dräger, Jinbo Xu
2021 Bioinformatics  
The Systems Biology Simulation Core Library (SBSCL) provides interpreters and solvers for these standards as a versatile open-source API in JavaTM.  ...  , including the Systems Biology Test Suite and published models from the BioModels and BiGG databases.  ...  Acknowledgements The authors acknowledge contributions by Nicolas Rodriguez, Alexander Dörr, Roland Keller, and the Harvey Mudd College for the ODEToolkit.  ... 
doi:10.1093/bioinformatics/btab669 pmid:34554191 pmcid:PMC8756180 fatcat:6bbmdjtlnrfuxdh7othwvwcxsy

Parallel stochastic systems biology in the cloud

M. Aldinucci, M. Torquati, C. Spampinato, M. Drocco, C. Misale, C. Calcagno, M. Coppo
2013 Briefings in Bioinformatics  
In particular, the Calculus of Wrapped Components (CWC) simulator for systems biology, which is designed according to the FastFlow pattern-based approach, is presented and discussed.  ...  The stochastic modelling of biological systems, coupled with Monte Carlo simulation of models, is an increasingly popular technique in bioinformatics.  ...  As the CWC simulator implements a Monte Carlo algorithm for systems biology, the issues for its portable and efficient design for the cloud are paradigmatic for a broad class of algorithms for Bioinformatics  ... 
doi:10.1093/bib/bbt040 pmid:23780997 fatcat:j4twwscdvbgjfl7ayapqsdzecu

Setting up a Meta-Threading Pipeline for High-Throughput Structural Bioinformatics: eThread Software Distribution, Walkthrough and Resource Profiling

Michal Brylinski
2013 Journal of computer science and systems biology  
area of systems biology.  ...  . eThread integrates a diverse collection of algorithms, therefore its deployment on a large multi-core system necessarily requires comprehensive profiling to ensure the optimal utilization of available  ...  Mark Jarrell and Juana Moreno, leaders of the LA-SiGMA GPU team (http://lasigma.loni.org/), for providing an access to testing systems equipped with Tesla M2050 and M2070 cards, and Mr.  ... 
doi:10.4172/jcsb.1000094 fatcat:kfma3ewdfngnxfw5iurakwuzkq

Specifications of Standards in Systems and Synthetic Biology: Status and Developments in 2016

Falk Schreiber, Gary D. Bader, Padraig Gleeson, Martin Golebiewski, Michael Hucka, Nicolas Le Novère, Chris Myers, David Nickerson, Björn Sommer, Dagmar Waltemath
2016 Journal of Integrative Bioinformatics  
SummaryStandards are essential to the advancement of science and technology. In systems and synthetic biology, numerous standards and associated tools have been developed over the last 16 years.  ...  This special issue of the Journal of Integrative Bioinformatics aims to support the exchange, distribution and archiving of these standards, as well as to provide centralised and easily citable access  ...  Kinetic Simulation Algorithm Ontology, to provide support for referring to specific simulation algorithms in descriptions of simulation experiments [29] .  ... 
doi:10.1515/jib-2016-289 fatcat:6dtmkxiz3jejvf3lrzjdjscxtu

Specifications of Standards in Systems and Synthetic Biology: Status and Developments in 2017

Falk Schreiber, Gary D. Bader, Padraig Gleeson, Martin Golebiewski, Michael Hucka, Sarah M. Keating, Nicolas Le Novère, Chris Myers, David Nickerson, Björn Sommer, Dagmar Waltemath
2018 Journal of Integrative Bioinformatics  
Standards are essential to the advancement of Systems and Synthetic Biology.  ...  The regular special issue of the Journal of Integrative Bioinformatics aims to support the exchange, distribution and archiving of these standards by providing unified, easily citable access.  ...  Kinetic Simulation Algorithm Ontology, to provide support for referring to specific simulation algorithms in descriptions of simulation experiments [29] .  ... 
doi:10.1515/jib-2018-0013 pmid:29596055 fatcat:prdywukrwzfitieltnzlu7rzj4

Exercising High-Level Parallel Programming on Streams: A Systems Biology Use Case

Marco Aldinucci, Maurizio Drocco, Guilherme Peretti Pezzi, Claudia Misale, Fabio Tordini, Massimo Torquati
2014 2014 IEEE 34th International Conference on Distributed Computing Systems Workshops  
In particular, the Calculus of Wrapped Compartments (CWC) parallel simulator for systems biology equipped with online mining of results, which is designed according to the FastFlow pattern-based approach  ...  The stochastic modelling of biological systems, coupled with Monte Carlo simulation of models, is an increasingly popular technique in Bioinformatics.  ...  INTRODUCTION Systems biology is a biology-based inter-disciplinary field that studies living organisms, considering them as systems whose evolution depends on how components interact among them.  ... 
doi:10.1109/icdcsw.2014.38 dblp:conf/icdcsw/AldinucciDPMTT14 fatcat:xxet3emit5catkev7xcunsq2e4

Taming the complexity of biological pathways through parallel computing

P. Ballarini, R. Guido, T. Mazza, D. Prandi
2008 Briefings in Bioinformatics  
of a system of ordinary differential equations (ODEs) or the simulation of a stochastic model, is commonly computed in a centralised fashion.  ...  In recent times, research efforts moved towards the definition of parallel/distributed algorithms as a means to tackle the complexity of biological models analysis.  ...  Parallel stochastic simulation Stochastic simulation approaches, such as the one implemented by the SSA, are not new in systems biology; however only in relatively recent times they have received much  ... 
doi:10.1093/bib/bbp020 pmid:19339382 fatcat:5yzyzsjbjvd2hb5rxufpg6hube

GPU accelerated biochemical network simulation

Yanxiang Zhou, Juliane Liepe, Xia Sheng, Michael P. H. Stumpf, Chris Barnes
2011 Computer applications in the biosciences : CABIOS  
Motivation: Mathematical modelling is central to systems and synthetic biology.  ...  Algorithms are implemented for the three popular types of model formalisms: the LSODA algorithm for ODE integration, the Euler-Maruyama algorithm for SDE simulation and the Gillespie algorithm for MJP  ...  INTRODUCTION Mathematical modelling is an integral part of systems and synthetic biology.  ... 
doi:10.1093/bioinformatics/btr015 pmid:21224286 pmcid:PMC3051321 fatcat:mcngxp5rgzaupgnmw6krpyvh7q

An efficient GPU acceptance-rejection algorithm for the selection of the next reaction to occur for Stochastic Simulation Algorithms [article]

Neri Mickael, Denis Mestivier
2014 arXiv   pre-print
Motivation: The Stochastic Simulation Algorithm (SSA) has largely diffused in the field of systems biology.  ...  This approach needs many realizations for establishing statistical results on the system under study.  ...  ACKNOWLEDGEMENT We would like to thank the NVIDIA Technology Center (PSG Cluster) for providing access to K10 and K20 GPU Cards.  ... 
arXiv:1404.0027v1 fatcat:bzjgla4iazh6xhcqrr2xdqp42q

Many-core CPUs can deliver scalable performance to stochastic simulations of large-scale biochemical reaction networks

Elias Kouskoumvekakis, Dimitrios Soudris, Elias S. Manolakos
2015 2015 International Conference on High Performance Computing & Simulation (HPCS)  
Stochastic simulation of large-scale biochemical reaction networks is becoming essential for Systems Biology.  ...  Method exact stochastic simulation algorithm.  ...  ACKNOWLEDGMENTS This research is implemented in the framework of operation "ΑRISTEIA II", which is co-funded by the European Union (European Social Fund) and national resources through the Operational  ... 
doi:10.1109/hpcsim.2015.7237084 dblp:conf/ieeehpcs/Kouskoumvekakis15 fatcat:4kr474ygizfuhps6qk3cyvacx4

Graphics processing units in bioinformatics, computational biology and systems biology

Marco S. Nobile, Paolo Cazzaniga, Andrea Tangherloni, Daniela Besozzi
2016 Briefings in Bioinformatics  
Several studies in Bioinformatics, Computational Biology and Systems Biology rely on the definition of physico-chemical or mathematical models of biological systems at different scales and levels of complexity  ...  CPU-based software, and allow more intensive investigations of biological systems.  ...  Biology and Systems Biology, emphasizing their advantages (i.e. computational speed-up) as well as drawbacks (e.g. the necessity of algorithm redesign and tailored implementation to fully leverage the  ... 
doi:10.1093/bib/bbw058 pmid:27402792 fatcat:oswcvoaqergwdkgss6w6tm25vi

Scalability Test of multiscale fluid–platelet model for three top supercomputers

Peng Zhang, Na Zhang, Chao Gao, Li Zhang, Yuxiang Gao, Yuefan Deng, Danny Bluestein
2016 Computer Physics Communications  
Utilizing current advanced HPC resources, the simulation rates achieved by our algorithms bring within reach performing complex multiscale simulations for solving vexing problems at the interface of biology  ...  Our implementations of multiple time-stepping (MTS) algorithm improved the performance of single time-stepping (STS) in all experiments.  ...  We customized the LAMMPS software suite to implement our new model and algorithm.  ... 
doi:10.1016/j.cpc.2016.03.019 pmid:27570250 pmcid:PMC4999248 fatcat:ekgld7lyorhcjlzkvvtd2mstvu

Minimum Information About a Simulation Experiment (MIASE)

Dagmar Waltemath, Richard Adams, Daniel A. Beard, Frank T. Bergmann, Upinder S. Bhalla, Randall Britten, Vijayalakshmi Chelliah, Michael T. Cooling, Jonathan Cooper, Edmund J. Crampin, Alan Garny, Stefan Hoops (+17 others)
2011 PLoS Computational Biology  
Advanced numerical algorithms and complex modeling workflows used in modern computational biology make reproduction of simulations difficult.  ...  Needs for a Standard Description of Simulations Experiments The rise of systems biology as a new paradigm of biological research has put computational modeling under the spotlight.  ...  Acknowledgments Authors are grateful to James Bassingthwaighte, Igor Goryanin, Fedor Kolpakov, and Benjamin Zaitlen for discussions and comments on the manuscript.  ... 
doi:10.1371/journal.pcbi.1001122 pmid:21552546 pmcid:PMC3084216 fatcat:6ihq7usih5fu7gpdmob25pcwaa
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